<macros>
    <token name="@VERSION@">2.2.2d</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">qualimap</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btv566</citation>
            <citation type="doi">10.1093/bioinformatics/bts503</citation>
            <yield />
        </citations>
    </xml>

    <token name="@SET_JAVA_OPTS@">
        export JAVA_OPTS="-Djava.awt.headless=true -Xmx\${GALAXY_MEMORY_MB:-1024}m"
    </token>

    <token name="@MASSAGE_OUTPUT@"><![CDATA[
        sed 's|images_${report_name}/||g;s|css/||g' results/${report_name}.html > '$output_html' &&
        mkdir '${output_html.extra_files_path}' &&
        mv results/css/*.css '${output_html.extra_files_path}' &&
        mv results/css/*.png '${output_html.extra_files_path}' &&
        if [ -d results/images_${report_name} ]; then
          mv results/images_${report_name}/* '${output_html.extra_files_path}' &&
          for file in \$(ls -A results/raw_data_${report_name}); do mv "results/raw_data_${report_name}/\$file" `echo "results/\$file" | sed 's/(//;s/)//'`; done
        fi
        #if $summary_report:
          && mv results/$summary_report results/summary_report.txt
        #end if
    ]]></token>
</macros>